Package index • metasalmon

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One-shot package creation from raw tables

create_sdp(): Create a Salmon Data Package directly from raw tables
infer_salmon_datapackage_artifacts(): Infer Salmon Data Package artifacts from resource tables
read_salmon_datapackage(): Read a Salmon Data Package

Advanced Package Assembly

Manual writing when you already have the SDP metadata tables assembled

write_salmon_datapackage(): Write a Salmon Data Package from preassembled metadata

Dictionary Functions

Infer, validate, and apply semantic data dictionaries

infer_dictionary(): Infer a starter dictionary from a data frame
validate_dictionary(): Validate a salmon data dictionary
apply_salmon_dictionary(): Apply a salmon dictionary to a data frame
apply_semantic_suggestions(): Apply semantic suggestions into a dictionary

Semantic Helpers

Semantic suggestion, vocabulary search, and ranking benchmark capabilities

suggest_semantics(): Suggest semantic annotations for a dictionary
find_terms(): Find candidate terms across external vocabularies
sources_for_role(): Get recommended sources for a given role
benchmark_term_ranking_fixtures(): Benchmark semantic term ranking against fixture cases
deduplicate_proposed_terms(): Deduplicate proposed ontology terms

Ontology + Validation

Fetch the ontology and validate semantic coverage

fetch_salmon_ontology(): Fetch the Salmon Domain Ontology with caching
validate_semantics(): Validate semantics with graceful gap reporting
suggest_facet_schemes(): Suggest facet schemes for proposed terms

Term Request Workflow

Detect missing SMN terms, route shared vs profile requests, and draft GitHub issues

detect_semantic_term_gaps(): Detect missing semantic terms that are not covered by SMN
render_ontology_term_request(): Render GitHub-ready ontology term request payloads
submit_term_request_issues(): Submit rendered ontology term requests as GitHub issues

NuSEDS Helpers

Crosswalk legacy NuSEDS method labels to canonical method families

nuseds_enumeration_method_crosswalk(): NuSEDS enumeration method crosswalk
nuseds_estimate_method_crosswalk(): NuSEDS estimate method crosswalk

Darwin Core (DwC-DP)

Darwin Core Data Package mapping and export helpers

suggest_dwc_mappings(): Suggest Darwin Core Data Package mappings for dictionary columns
dwc_dp_build_descriptor(): Build a DwC-DP datapackage descriptor (export helper)

Enterprise Data Hub (EDH)

HNAP-aware EDH XML export helper with legacy ISO 19139 fallback

edh_build_iso19139_xml(): Build ISO 19139 or HNAP-aware metadata XML for DFO Enterprise Data Hub export

GitHub Access

Authenticate once and read CSVs from private GitHub repositories

ms_setup_github(): Set up GitHub access for private repositories
github_raw_url(): Build a stable raw GitHub URL
read_github_csv(): Read a CSV from a GitHub repository
read_github_csv_dir(): Read all CSV files from a GitHub directory

ICES Vocabulary

Access ICES reference codes and vocabulary

ices_vocab: ICES controlled vocabularies (code lists)
ices_code_types(): List ICES code types
ices_codes(): List ICES codes for a code type
ices_find_code_types(): Find ICES code types by text match
ices_find_codes(): Find ICES codes within a code type by text match

Maintenance

Version and update helpers

check_for_updates(): Check whether a newer metasalmon release is available